[Bioc-sig-seq] readAligned and BAM format

[Pratap, Abhishek]

If following a hint that I should move to R-devel for testing RSamtools.

This is while trying to install RSAMTools

Warning in .completeClassSlots(ClassDef, where) :
  undefined slot classes in definition of "Alignments0":
gapped_ranges(class "GappedRanges")
Error in setValidity2("Alignments0", .valid.Alignments0, where =
asNamespace("Rsamtools")) : 
  unused argument(s) (where = asNamespace("Rsamtools"))
Error : unable to load R code in package 'Rsamtools'
ERROR: lazy loading failed for package 'Rsamtools'
* removing
'/local/projects/grc/devel/apratap/softwares/R-2.10.0/lib64/R/library/Rs
amtools


-Abhi

-----Original Message-----
From: bioc-sig-sequencing-bounces at r-project.org
[mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Pratap,
Abhishek
Sent: Tuesday, December 08, 2009 5:20 PM
To: Martin Morgan
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] readAligned and BAM format

Thanks Martin. Clearly shows I am just getting started :).

-Abhi

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Tuesday, December 08, 2009 5:17 PM
To: Pratap, Abhishek
Cc: Wu Wei; bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] readAligned and BAM format

Pratap, Abhishek wrote:
> Hi Martin
> 
> Just wondering if people outside the firewall/network without passw
> could download this package ?

Hi Abhi -- there are short instructions on use of svn, including
password, at

  http://wiki.fhcrc.org/bioc/SvnHowTo

Important to note that this package is very much under active
development, so subject to frequent and unpredictable change.

Martin

> 
> 
> Thanks,
> -Abhi 
> 
> -----Original Message-----
> From: bioc-sig-sequencing-bounces at r-project.org
> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Martin
> Morgan
> Sent: Monday, November 02, 2009 8:58 AM
> To: Wu Wei
> Cc: bioc-sig-sequencing at r-project.org
> Subject: Re: [Bioc-sig-seq] readAligned and BAM format
> 
> Hi Wave --
> 
> svn co
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
> 
> R CMD INSTALL --clean Rsamtools
> 
> see the script in Rsamtools/inst/script/readAligned_prototype.R
> 
> e.g.,
> 
>   source(system.file("script", "readAligned_prototype.R",
>                      package="Rsamtools"))
>   .readAligned_bam(<...>) # args like the other readAligned
> 
> see ?scanBam for additional ideas.
> 
> Martin
> 
> Wu Wei wrote:
>> Hi Martin,
>>
>> I am also looking for that. Would you please also forward that
>> additional info to me.
>>
>> Thanks,
>> Wave
>>
>> On 2 Nov 2009, at 14:34, Martin Morgan wrote:
>>
>>> Joern Toedling wrote:
>>>> Hi everyone,
>>>>
>>>> has anybody by chance already written a parser for importing
>>>> alignments in
>>>> BAM/SAM format into objects of class AlignedRead? This format seems
>>>> to be
>>>> gaining more and more support, yet it is still absent from the
>>>> options in
>>>> function readAligned. If one of you already has written such a
> parsing
>>>> function and would not mind sharing it, please let me know.
>>> Hi Joern -- there is a package in the Bioc svn repository that does
>>> this; it is not yet in the devel branch, there are some limitations
> in
>>> terms of AlignedRead (e.g., AlignedRead currently supports only
> ungapped
>>> alignments, whereas BAM allows gapped). I'll forward additional info
>>> off-list.
>>>
>>> Martin
>>>> Best regards,
>>>> Joern
>>>>
>>>> ---
>>>> Joern Toedling
>>>> Institut Curie -- U900
>>>> 26 rue d'Ulm, 75005 Paris, FRANCE
>>>> Tel. +33 (0)156246926
>>>>
>>>> _______________________________________________
>>>> Bioc-sig-sequencing mailing list
>>>> Bioc-sig-sequencing at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>> -- 
>>> Martin Morgan
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>> Wu Wei
>> Postdoctoral Fellow
>> Steinmetz Group, EMBL Heidelberg
>> Tex: +49 6221 387-8310 (8114)
>> Fax: +49 6221 387-8518
>> Email: wuwei at embl.de
>>
>>
>>
>>
> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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